Rockstar Games warned users of Grand Theft Auto V (GTA V) about cars disappearing when you park in garages and they are fixing the bug at the moment.
The company said that they are looking into a glitch that sometimes causes cars to lose upgrades or completely disappear from safe houses.
In their support forum developers said they are fixing the problem:
"We have received some reports about problems with cars and garages, particularly after upgrading and then completing a mission, and are looking into this now. Unfortunately, we do not currently have a workaround to recover a car if it is missing. If you would like to receive an automatic email notification as soon as there is more information, please log into the Support Site and click Subscribe at the top of this page.
Also please note that vehicles saves in the garage of one safehouse (Franklin's Aunt's) may not show up in the garage of a different safehouse (Franklin's Vinewood Hills)."
"Update for 9/22/13: This issue may occur if you drive another character’s personal vehicle. We are looking into a fix to prevent this from occurring in the future. If you would like to receive an automatic email notification when the fix is live, please log into the Support Site and click Subscribe at the top of this page. In the meantime, please try to avoid parking a car in a garage, driving one already in a garage, or getting in a default vehicle, when playing as a character other than the one with your upgrades."
Rockstar suggested players should subscribe to their support site feed for automatic updates on the issue.
